Dicty analysis
summary
Summary statistics Dicty
## # A tibble: 15 x 3
## # Groups: bait [12]
## bait condition Unique_bait
## <fct> <fct> <int>
## 1 Galpha2 starv 1
## 2 Galpha2 veg 1
## 3 Galpha4 Normal 1
## 4 Galpha8 GDP 1
## 5 Galpha8 GppNHp 1
## 6 Galpha8 Normal 1
## 7 Gbeta1 Normal 1
## 8 Gbeta2 Normal 1
## 9 Rac1 Normal 1
## 10 RapA Normal 1
## 11 RasB Normal 1
## 12 RasC Normal 1
## 13 RasG1 Normal 1
## 14 Ric8 Normal 1
## 15 Roco4 BACKGROUND 1Show the unique baits count
## # A tibble: 1 x 1
## Unique_bait_condition
## <int>
## 1 15Show how many instances (lines) of bait there are
##
## Galpha2 Galpha4 Galpha8 Gbeta1 Gbeta2 Rac1 RapA RasB RasC RasG1
## 3206 1603 4100 876 876 1448 461 808 998 337
## Ric8 Roco4
## 1448 1448Show how many instances (lines) of condition there are
##
## BACKGROUND GDP GppNHp Normal starv veg
## 1448 1436 1436 10083 1603 1603Show total spectral count per bait + condition
## # A tibble: 15 x 3
## bait condition spectral_count
## <fct> <fct> <dbl>
## 1 Galpha2 starv 20155
## 2 Galpha2 veg 30986
## 3 Galpha4 Normal 27070
## 4 Galpha8 GDP 13099
## 5 Galpha8 GppNHp 23136
## 6 Galpha8 Normal 23324
## 7 Gbeta1 Normal 16390
## 8 Gbeta2 Normal 20644
## 9 Rac1 Normal 22196
## 10 RapA Normal 5238
## 11 RasB Normal 12182
## 12 RasC Normal 22778
## 13 RasG1 Normal 12369
## 14 Ric8 Normal 18323
## 15 Roco4 BACKGROUND 19376Show normalized spectral count per bait + condition
## # A tibble: 15 x 3
## bait condition z_score_spectral
## <fct> <fct> <dbl>
## 1 Galpha2 starv 9.37e-16
## 2 Galpha2 veg 1.30e-14
## 3 Galpha4 Normal 7.91e-16
## 4 Galpha8 GDP -2.50e-14
## 5 Galpha8 GppNHp 4.31e-14
## 6 Galpha8 Normal 1.87e-14
## 7 Gbeta1 Normal 1.72e-14
## 8 Gbeta2 Normal 7.63e-15
## 9 Rac1 Normal 7.24e-15
## 10 RapA Normal -1.07e-14
## 11 RasB Normal 1.05e-14
## 12 RasC Normal -2.95e-15
## 13 RasG1 Normal -4.02e-15
## 14 Ric8 Normal -4.04e-15
## 15 Roco4 BACKGROUND 1.28e-15Show how many uniq uniprot id’s are in the set (dicty has 6 chromosomes and 12500 proteins)
## [1] 2988uniq proteins per bait_condition
## # A tibble: 15 x 3
## # Groups: bait [12]
## bait condition `n_distinct(uniprot)`
## <fct> <fct> <int>
## 1 Galpha2 starv 1603
## 2 Galpha2 veg 1603
## 3 Galpha4 Normal 1603
## 4 Galpha8 GDP 1436
## 5 Galpha8 GppNHp 1436
## 6 Galpha8 Normal 1228
## 7 Gbeta1 Normal 876
## 8 Gbeta2 Normal 876
## 9 Rac1 Normal 1448
## 10 RapA Normal 461
## 11 RasB Normal 808
## 12 RasC Normal 998
## 13 RasG1 Normal 337
## 14 Ric8 Normal 1448
## 15 Roco4 BACKGROUND 1448Unique proteins per condition
## # A tibble: 6 x 2
## condition `n_distinct(uniprot)`
## <fct> <int>
## 1 BACKGROUND 1448
## 2 GDP 1436
## 3 GppNHp 1436
## 4 Normal 2933
## 5 starv 1603
## 6 veg 1603Unique proteins per bait
## # A tibble: 12 x 2
## bait `n_distinct(uniprot)`
## <fct> <int>
## 1 Galpha2 1603
## 2 Galpha4 1603
## 3 Galpha8 1446
## 4 Gbeta1 876
## 5 Gbeta2 876
## 6 Rac1 1448
## 7 RapA 461
## 8 RasB 808
## 9 RasC 998
## 10 RasG1 337
## 11 Ric8 1448
## 12 Roco4 1448absolute spectral count
Barplot showing the total spectral count for each bait 
Barplot showing the absolute spectral count for each condition 
Combined spectral count for bait + condition, sum spectral count per group 
average spectra
Barplot showing the average spectral count per protein for each bait divided the summed group count by the number of observations in that group so avg count per group 
Barplot showing the average spectral count for each condition: divided the summed group count by the number of observations in that group, 
Combined spectral count for bait + condition, average spectral count per group 
Combined spectral count for bait + condition, average spectral count per group Add overlay with unique proteins 
boxplot bait absolute count
Boxplot absolute count vs bait 
boxplot condition absolute count
Boxplot count vs condition 
boxplot experiment absolute count
Boxplot combined spectral count for bait + condition 
z-score normalized boxplot count vs bait
z-score normalized boxplot count vs condition
boxplot count vs condition 
z-score normalized boxplot boxplot count vs experiment
Venn diagrams
Venn diagrams over bait
Venn diagrams over condition
overlap proteins per bait_condition
Method to retrieve the overlapping proteins per experiment
Presence/absence protein
Heatmap for uniprot presence/absence over bait, condition or experiment. Filtered on protein 
Overlapping proteins
## Galpha2_starv Galpha2_veg Galpha4_Normal Galpha8_GDP
## Galpha2_starv 1603 1603 1603 1059
## Galpha2_veg 1603 1603 1603 1059
## Galpha4_Normal 1603 1603 1603 1059
## Galpha8_GDP 1059 1059 1059 1436
## Galpha8_GppNHp 1059 1059 1059 1436
## Galpha8_Normal 957 957 957 1218
## Gbeta1_Normal 736 736 736 739
## Gbeta2_Normal 736 736 736 739
## Rac1_Normal 1098 1098 1098 1131
## RapA_Normal 0 0 0 0
## RasB_Normal 609 609 609 567
## RasC_Normal 759 759 759 649
## RasG1_Normal 279 279 279 247
## Ric8_Normal 1098 1098 1098 1131
## Roco4_BACKGROUND 1098 1098 1098 1131
## Galpha8_GppNHp Galpha8_Normal Gbeta1_Normal Gbeta2_Normal
## Galpha2_starv 1059 957 736 736
## Galpha2_veg 1059 957 736 736
## Galpha4_Normal 1059 957 736 736
## Galpha8_GDP 1436 1218 739 739
## Galpha8_GppNHp 1436 1218 739 739
## Galpha8_Normal 1218 1228 692 692
## Gbeta1_Normal 739 692 876 876
## Gbeta2_Normal 739 692 876 876
## Rac1_Normal 1131 1015 749 749
## RapA_Normal 0 0 0 0
## RasB_Normal 567 515 443 443
## RasC_Normal 649 586 526 526
## RasG1_Normal 247 220 217 217
## Ric8_Normal 1131 1015 749 749
## Roco4_BACKGROUND 1131 1015 749 749
## Rac1_Normal RapA_Normal RasB_Normal RasC_Normal RasG1_Normal
## Galpha2_starv 1098 0 609 759 279
## Galpha2_veg 1098 0 609 759 279
## Galpha4_Normal 1098 0 609 759 279
## Galpha8_GDP 1131 0 567 649 247
## Galpha8_GppNHp 1131 0 567 649 247
## Galpha8_Normal 1015 0 515 586 220
## Gbeta1_Normal 749 0 443 526 217
## Gbeta2_Normal 749 0 443 526 217
## Rac1_Normal 1448 0 577 679 264
## RapA_Normal 0 461 0 0 0
## RasB_Normal 577 0 808 570 241
## RasC_Normal 679 0 570 998 300
## RasG1_Normal 264 0 241 300 337
## Ric8_Normal 1448 0 577 679 264
## Roco4_BACKGROUND 1448 0 577 679 264
## Ric8_Normal Roco4_BACKGROUND
## Galpha2_starv 1098 1098
## Galpha2_veg 1098 1098
## Galpha4_Normal 1098 1098
## Galpha8_GDP 1131 1131
## Galpha8_GppNHp 1131 1131
## Galpha8_Normal 1015 1015
## Gbeta1_Normal 749 749
## Gbeta2_Normal 749 749
## Rac1_Normal 1448 1448
## RapA_Normal 0 0
## RasB_Normal 577 577
## RasC_Normal 679 679
## RasG1_Normal 264 264
## Ric8_Normal 1448 1448
## Roco4_BACKGROUND 1448 1448## [1] 279Simple heatmap with clustering on overlapping proteins per experiment
ggplot heatmap overlapping proteins per experiment
Correlations
raw data
bait heatmap on raw spectra correlation
Condition heatmap on raw spectra correlation
Experiment heatmap on raw spectra correlation
Normalized data
Bait heatmap on normalized spectra correlation
Condition heatmap on normalized spectra correlation
Experiment heatmap on normalized spectra correlation
PCA
bait on raw spectral_count
## Importance of components:
## PC1 PC2 PC3 PC4 PC5
## Standard deviation 2500.4102 1578.8117 1143.0789 929.48826 767.77013
## Proportion of Variance 0.4999 0.1993 0.1045 0.06908 0.04713
## Cumulative Proportion 0.4999 0.6992 0.8036 0.87271 0.91984
## PC6 PC7 PC8 PC9 PC10
## Standard deviation 677.44725 462.20211 411.55101 320.37644 209.71468
## Proportion of Variance 0.03669 0.01708 0.01354 0.00821 0.00352
## Cumulative Proportion 0.95654 0.97362 0.98716 0.99537 0.99888
## PC11 PC12
## Standard deviation 118.26325 1.295e-11
## Proportion of Variance 0.00112 0.000e+00
## Cumulative Proportion 1.00000 1.000e+00
Condition on raw spectral_count
## Importance of components:
## PC1 PC2 PC3 PC4 PC5
## Standard deviation 7191.7321 2542.4427 722.60547 539.67106 361.21598
## Proportion of Variance 0.8747 0.1093 0.00883 0.00493 0.00221
## Cumulative Proportion 0.8747 0.9840 0.99287 0.99779 1.00000
## PC6
## Standard deviation 1.66e-11
## Proportion of Variance 0.00e+00
## Cumulative Proportion 1.00e+00
Experiment (bait + condition) on raw spectral_count
## Importance of components:
## PC1 PC2 PC3 PC4 PC5
## Standard deviation 1971.9458 1290.9757 838.30393 756.25286 636.05050
## Proportion of Variance 0.4743 0.2033 0.08572 0.06976 0.04935
## Cumulative Proportion 0.4743 0.6776 0.76331 0.83307 0.88242
## PC6 PC7 PC8 PC9 PC10
## Standard deviation 595.58323 440.54269 371.26426 355.02771 265.38000
## Proportion of Variance 0.04327 0.02367 0.01681 0.01537 0.00859
## Cumulative Proportion 0.92569 0.94936 0.96617 0.98154 0.99013
## PC11 PC12 PC13 PC14 PC15
## Standard deviation 204.91780 171.32312 93.43430 28.3651 5.069e-12
## Proportion of Variance 0.00512 0.00358 0.00106 0.0001 0.000e+00
## Cumulative Proportion 0.99526 0.99884 0.99990 1.0000 1.000e+00
Igraph network plot
Demo Viz functions
